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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 14 | Line 21
21
22		// some defines for ensemble and Forcefield  cases
23
24	<	#define NVE_ENS   0
25	<	#define NVT_ENS   1
26	<	#define NPTi_ENS  2
27	<	#define NPTf_ENS  3
28	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
24	>	#define NVE_ENS        0
25	>	#define NVT_ENS        1
26	>	#define NPTi_ENS       2
27	>	#define NPTf_ENS       3
28	>	#define NPTxyz_ENS     4
29
30
31	<	#define FF_DUFF 0
32	<	#define FF_LJ   1
31	>	#define FF_DUFF  0
32	>	#define FF_LJ    1
33	>	#define FF_EAM   2
34	>	#define FF_H2O   3
35
36	+	using namespace std;
37
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 41 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
127	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
131	>	// creation of complex system objects
132
133	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
133	>	sysObjectsCreation();
134
135	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
135	>	// check on the post processing info
136
137	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
137	>	finalInfoCheck();
138
139	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
133	<	}
134	<	strcpy( simnfo->ensemble, ensemble );
139	>	// initialize the system coordinates
140
141	+	if ( !initSuspend ){
142	+	initSystemCoords();
143
144	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
145	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
146	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146	>	}
147
148	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
148	>	// make the output filenames
149
150	<	//     if (the_globals->haveTauBarostat())
151	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
152	<	//     else {
153	<	//       sprintf( painCave.errMsg,
154	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
150	>	makeOutNames();
151	>
152	>	#ifdef IS_MPI
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
156	>	// initialize the Fortran
157
158	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
158	>	initFortran();
159
160	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
161	<	simnfo->usePBC = the_globals->getPBC();
162	<
163	<	int usesDipoles = 0;
164	<	switch( ffCase ){
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	case FF_DUFF:
199	<	the_ff = new DUFF();
200	<	usesDipoles = 1;
201	<	break;
167	>	}
168
203	–	case FF_LJ:
204	–	the_ff = new LJFF();
205	–	break;
169
170	<	default:
171	<	sprintf( painCave.errMsg,
172	<	"SimSetup Error. Unrecognized force field in case statement.\n");
173	<	painCave.isFatal = 1;
174	<	simError();
175	<	}
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
176	>	molInit molInfo;
177	>	DirectionalAtom* dAtom;
178	>	RigidBody* myRB;
179	>	StuntDouble* mySD;
180	>	LinkedAssign* extras;
181	>	LinkedAssign* current_extra;
182	>	AtomStamp* currentAtom;
183	>	BondStamp* currentBond;
184	>	BendStamp* currentBend;
185	>	TorsionStamp* currentTorsion;
186	>	RigidBodyStamp* currentRigidBody;
187	>	CutoffGroupStamp* currentCutoffGroup;
188	>	CutoffGroup* myCutoffGroup;
189	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192	<	#ifdef IS_MPI
193	<	strcpy( checkPointMsg, "ForceField creation successful" );
194	<	MPIcheckPoint();
217	<	#endif // is_mpi
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	// get the components and calculate the tot_nMol and indvidual n_mol
220	<	the_components = the_globals->getComponents();
221	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
196	>	set<int> skipList;
197
198	<	if( !the_globals->haveNMol() ){
199	<	// we don't have the total number of molecules, so we assume it is
200	<	// given in each component
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201
202	<	tot_nmol = 0;
203	<	for( i=0; i<n_components; i++ ){
202	>	//ConstraintPair* consPair; //constraint pair
203	>	//ConstraintElement* consElement1;  //first element of constraint pair
204	>	//ConstraintElement* consElement2;  //second element of constraint pair
205	>	//int whichRigidBody;
206	>	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	>	//vector<pair<int, int> > jointAtoms;
208	>	//init the forceField paramters
209
210	<	if( !the_components[i]->haveNMol() ){
211	<	// we have a problem
212	<	sprintf( painCave.errMsg,
234	<	"SimSetup Error. No global NMol or component NMol"
235	<	" given. Cannot calculate the number of atoms.\n" );
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	}
210	>	the_ff->readParams();
211	>
212	>	// init the atoms
213
214	<	tot_nmol += the_components[i]->getNMol();
241	<	components_nmol[i] = the_components[i]->getNMol();
242	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
214	>	int nMembers, nNew, rb1, rb2;
215
216	+	for (k = 0; k < nInfo; k++){
217	+	the_ff->setSimInfo(&(info[k]));
218	+
219		#ifdef IS_MPI
220	<	strcpy( checkPointMsg, "Have the number of components" );
221	<	MPIcheckPoint();
222	<	#endif // is_mpi
220	>	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	>	info[k].globalGroupMembership[i] = 0;
223	>	#else
224	>	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	>	for (i = 0; i < info[k].n_atoms; i++)
226	>	info[k].globalGroupMembership[i] = 0;
227	>	#endif
228
229	<	// make an array of molecule stamps that match the components used.
230	<	// also extract the used stamps out into a separate linked list
229	>	atomOffset = 0;
230	>	groupOffset = 0;
231
232	<	simnfo->nComponents = n_components;
233	<	simnfo->componentsNmol = components_nmol;
234	<	simnfo->compStamps = comp_stamps;
280	<	simnfo->headStamp = new LinkedMolStamp();
281	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
232	>	for (i = 0; i < info[k].n_mol; i++){
233	>	stampID = info[k].molecules[i].getStampID();
234	>	molName = comp_stamps[stampID]->getID();
235
236	<	id = the_components[i]->getType();
237	<	comp_stamps[i] = NULL;
238	<
239	<	// check to make sure the component isn't already in the list
236	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
239	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241
242	<	comp_stamps[i] = headStamp->match( id );
293	<	if( comp_stamps[i] == NULL ){
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243
244	<	// extract the component from the list;
296	<
297	<	currentStamp = the_stamps->extractMolStamp( id );
298	<	if( currentStamp == NULL ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
244	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
245
246	<	#ifdef IS_MPI
247	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
248	<	MPIcheckPoint();
249	<	#endif // is_mpi
316	<
246	>	if (molInfo.nBonds > 0)
247	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	>	else
249	>	molInfo.myBonds = NULL;
250
251	+	if (molInfo.nBends > 0)
252	+	molInfo.myBends = new Bend*[molInfo.nBends];
253	+	else
254	+	molInfo.myBends = NULL;
255
256	+	if (molInfo.nTorsions > 0)
257	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	+	else
259	+	molInfo.myTorsions = NULL;
260
261	<	// caclulate the number of atoms, bonds, bends and torsions
261	>	theBonds = new bond_pair[molInfo.nBonds];
262	>	theBends = new bend_set[molInfo.nBends];
263	>	theTorsions = new torsion_set[molInfo.nTorsions];
264	>
265	>	// make the Atoms
266
267	<	tot_atoms = 0;
268	<	tot_bonds = 0;
324	<	tot_bends = 0;
325	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
327	<
328	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
267	>	for (j = 0; j < molInfo.nAtoms; j++){
268	>	currentAtom = comp_stamps[stampID]->getAtom(j);
269
270	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
270	>	if (currentAtom->haveOrientation()){
271	>	dAtom = new DirectionalAtom((j + atomOffset),
272	>	info[k].getConfiguration());
273	>	info[k].n_oriented++;
274	>	molInfo.myAtoms[j] = dAtom;
275
276	<	simnfo->n_atoms = tot_atoms;
277	<	simnfo->n_bonds = tot_bonds;
278	<	simnfo->n_bends = tot_bends;
339	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
342	<
343	<	simnfo->molMembershipArray = new int[tot_atoms];
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279
280	<	#ifdef IS_MPI
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283
284	<	// divide the molecules among processors here.
285	<
286	<	mpiSim = new mpiSimulation( simnfo );
287	<
351	<	globalIndex = mpiSim->divideLabor();
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286	>	}
287	>	else{
288
289	<	// set up the local variables
354	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290
291	<	int* mol2proc = mpiSim->getMolToProcMap();
359	<	int* molCompType = mpiSim->getMolComponentType();
360	<
361	<	allMol = 0;
362	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
291	>	}
292
293	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
294	+	#ifdef IS_MPI
295	+	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296	+	#endif // is_mpi
297	+	}
298
299	<	for( i=0; i<n_components; i++ ){
299	>	// make the bonds
300	>	for (j = 0; j < molInfo.nBonds; j++){
301	>	currentBond = comp_stamps[stampID]->getBond(j);
302	>	theBonds[j].a = currentBond->getA() + atomOffset;
303	>	theBonds[j].b = currentBond->getB() + atomOffset;
304
305	<	for( j=0; j<components_nmol[i]; j++ ){
306	<
374	<	if( mol2proc[allMol] == worldRank ){
375	<
376	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
385	<	}
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307
308	<	allMol++;
309	<	}
310	<	}
311	<	local_SRI = local_bonds + local_bends + local_torsions;
312	<
313	<	simnfo->n_atoms = mpiSim->getMyNlocal();
314	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
308	>	#ifdef IS_MPI
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315
316	<	simnfo->n_bonds = local_bonds;
317	<	simnfo->n_bends = local_bends;
406	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
316	>	info[k].excludes->addPair(exI, exJ);
317	>	}
318
319	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
320	<	MPIcheckPoint();
321	<
322	<
323	<	#endif // is_mpi
324	<
319	>	//make the bends
320	>	for (j = 0; j < molInfo.nBends; j++){
321	>	currentBend = comp_stamps[stampID]->getBend(j);
322	>	theBends[j].a = currentBend->getA() + atomOffset;
323	>	theBends[j].b = currentBend->getB() + atomOffset;
324	>	theBends[j].c = currentBend->getC() + atomOffset;
325
326	<	// create the atom and short range interaction arrays
326	>	if (currentBend->haveExtras()){
327	>	extras = currentBend->getExtras();
328	>	current_extra = extras;
329
330	<	Atom::createArrays(simnfo->n_atoms);
331	<	the_atoms = new Atom*[simnfo->n_atoms];
332	<	the_molecules = new Molecule[simnfo->n_mol];
333	<	int molIndex;
334	<
335	<	// initialize the molecule's stampID's
330	>	while (current_extra != NULL){
331	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
332	>	switch (current_extra->getType()){
333	>	case 0:
334	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
335	>	theBends[j].isGhost = 1;
336	>	break;
337
338	+	case 1:
339	+	theBends[j].ghost = (int) current_extra->getDouble() +
340	+	atomOffset;
341	+	theBends[j].isGhost = 1;
342	+	break;
343	+
344	+	default:
345	+	sprintf(painCave.errMsg,
346	+	"SimSetup Error: ghostVectorSource was neither a "
347	+	"double nor an int.\n"
348	+	"-->Bend[%d] in %s\n",
349	+	j, comp_stamps[stampID]->getID());
350	+	painCave.isFatal = 1;
351	+	simError();
352	+	}
353	+	}
354	+	else{
355	+	sprintf(painCave.errMsg,
356	+	"SimSetup Error: unhandled bend assignment:\n"
357	+	"    -->%s in Bend[%d] in %s\n",
358	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
359	+	painCave.isFatal = 1;
360	+	simError();
361	+	}
362	+
363	+	current_extra = current_extra->getNext();
364	+	}
365	+	}
366	+
367	+	if (theBends[j].isGhost) {
368	+
369	+	tempI = theBends[j].a;
370	+	tempJ = theBends[j].b;
371	+
372		#ifdef IS_MPI
373	<
373	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	#endif
379	>	info[k].excludes->addPair(exI, exJ);
380
381	<	molIndex = 0;
430	<	for(i=0; i<mpiSim->getTotNmol(); i++){
431	<
432	<	if(mol2proc[i] == worldRank ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
381	>	} else {
382
383	<	#else // is_mpi
384	<
385	<	molIndex = 0;
386	<	globalAtomIndex = 0;
387	<	for(i=0; i<n_components; i++){
388	<	for(j=0; j<components_nmol[i]; j++ ){
389	<	the_molecules[molIndex].setStampID( i );
390	<	the_molecules[molIndex].setMyIndex( molIndex );
391	<	the_molecules[molIndex].setGlobalIndex( molIndex );
392	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
393	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
394	<	globalAtomIndex++;
383	>	tempI = theBends[j].a;
384	>	tempJ = theBends[j].b;
385	>	tempK = theBends[j].c;
386	>
387	>	#ifdef IS_MPI
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395	>	#endif
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401		}
453	–	molIndex++;
454	–	}
455	–	}
456	–
402
403	<	#endif // is_mpi
403	>	for (j = 0; j < molInfo.nTorsions; j++){
404	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
405	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
406	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
407	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
408	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
409
410	+	tempI = theTorsions[j].a;
411	+	tempJ = theTorsions[j].b;
412	+	tempK = theTorsions[j].c;
413	+	tempL = theTorsions[j].d;
414
415	<	if( simnfo->n_SRI ){
416	<
417	<	Exclude::createArray(simnfo->n_SRI);
418	<	the_excludes = new Exclude*[simnfo->n_SRI];
419	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
420	<	simnfo->globalExcludes = new int;
421	<	simnfo->n_exclude = simnfo->n_SRI;
422	<	}
423	<	else{
424	<
425	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
415	>	#ifdef IS_MPI
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420	>	#else
421	>	exI = tempI + 1;
422	>	exJ = tempJ + 1;
423	>	exK = tempK + 1;
424	>	exL = tempL + 1;
425	>	#endif
426
427	<	// set the arrays into the SimInfo object
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433	>	}
434
435	<	simnfo->atoms = the_atoms;
436	<	simnfo->molecules = the_molecules;
437	<	simnfo->nGlobalExcludes = 0;
438	<	simnfo->excludes = the_excludes;
435	>
436	>	molInfo.myRigidBodies.clear();
437	>
438	>	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	+	nMembers = currentRigidBody->getNMembers();
442
443	<	// get some of the tricky things that may still be in the globals
443	>	// Create the Rigid Body:
444
445	<	double boxVector[3];
491	<	if( the_globals->haveBox() ){
492	<	boxVector[0] = the_globals->getBox();
493	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
445	>	myRB = new RigidBody();
446
447	<	double vol;
448	<	vol = (double)tot_nmol / the_globals->getDensity();
449	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
450	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
447	>	sprintf(rbName,"%s_RB_%d", molName, j);
448	>	myRB->setType(rbName);
449	>
450	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
451
452	<	simnfo->setBox( boxVector );
453	<	}
508	<	else{
509	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
452	>	// molI is atom numbering inside this molecule
453	>	molI = currentRigidBody->getMember(rb1);
454
455	<	if( !the_globals->haveBoxY() ){
456	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxY size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
455	>	// tempI is atom numbering on local processor
456	>	tempI = molI + atomOffset;
457
458	<	if( !the_globals->haveBoxZ() ){
459	<	sprintf( painCave.errMsg,
460	<	"SimSetup error, no periodic BoxZ size given.\n" );
528	<	painCave.isFatal = 1;
529	<	simError();
530	<	}
531	<	boxVector[2] = the_globals->getBoxZ();
458	>	// currentAtom is the AtomStamp (which we need for
459	>	// rigid body reference positions)
460	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
461
462	<	simnfo->setBox( boxVector );
463	<	}
462	>	// When we add to the rigid body, add the atom itself and
463	>	// the stamp info:
464
465	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	+
467	+	// Add this atom to the Skip List for the integrators
468		#ifdef IS_MPI
469	<	strcpy( checkPointMsg, "Box size set up" );
470	<	MPIcheckPoint();
471	<	#endif // is_mpi
469	>	slI = info[k].atoms[tempI]->getGlobalIndex();
470	>	#else
471	>	slI = tempI;
472	>	#endif
473	>	skipList.insert(slI);
474	>
475	>	}
476	>
477	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	>
480	>	tempI = currentRigidBody->getMember(rb1);
481	>	tempJ = currentRigidBody->getMember(rb2);
482	>
483	>	// Some explanation is required here.
484	>	// Fortran indexing starts at 1, while c indexing starts at 0
485	>	// Also, in parallel computations, the GlobalIndex is
486	>	// used for the exclude list:
487	>
488	>	#ifdef IS_MPI
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	>	#else
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	>	#endif
495	>
496	>	info[k].excludes->addPair(exI, exJ);
497	>
498	>	}
499	>	}
500
501	+	molInfo.myRigidBodies.push_back(myRB);
502	+	info[k].rigidBodies.push_back(myRB);
503	+	}
504	+
505
506	<	// initialize the arrays
506	>	//create cutoff group for molecule
507
508	<	the_ff->setSimInfo( simnfo );
508	>	cutoffAtomSet.clear();
509	>	molInfo.myCutoffGroups.clear();
510	>
511	>	for (j = 0; j < nCutoffGroups; j++){
512
513	<	makeMolecules();
514	<	simnfo->identArray = new int[simnfo->n_atoms];
548	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
513	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	>	nMembers = currentCutoffGroup->getNMembers();
515
516	<	if( !the_globals->haveEST() ){
517	<	sprintf( painCave.errMsg,
573	<	"SimSetup Warning: using default value of 0.05 * the "
574	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
575	<	);
576	<	painCave.isFatal = 0;
577	<	simError();
578	<	simnfo->est = 0.05 * simnfo->ecr;
579	<	} else {
580	<	simnfo->est        = the_globals->getEST();
581	<	}
582	<
583	<	if(!the_globals->haveDielectric() ){
584	<	sprintf( painCave.errMsg,
585	<	"SimSetup Error: You are trying to use Reaction Field without"
586	<	"setting a dielectric constant!\n"
587	<	);
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
591	<	simnfo->dielectric = the_globals->getDielectric();
592	<	} else {
593	<	if (usesDipoles) {
594	<
595	<	if( !the_globals->haveECR() ){
596	<	sprintf( painCave.errMsg,
597	<	"SimSetup Warning: using default value of 1/2 the smallest "
598	<	"box length for the electrostaticCutoffRadius.\n"
599	<	"I hope you have a very fast processor!\n");
600	<	painCave.isFatal = 0;
601	<	simError();
602	<	double smallest;
603	<	smallest = simnfo->boxLx;
604	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606	<	simnfo->ecr = 0.5 * smallest;
607	<	} else {
608	<	simnfo->ecr        = the_globals->getECR();
609	<	}
610	<
611	<	if( !the_globals->haveEST() ){
612	<	sprintf( painCave.errMsg,
613	<	"SimSetup Warning: using default value of 5%% of the "
614	<	"electrostaticCutoffRadius for the "
615	<	"electrostaticSkinThickness\n"
616	<	);
617	<	painCave.isFatal = 0;
618	<	simError();
619	<	simnfo->est = 0.05 * simnfo->ecr;
620	<	} else {
621	<	simnfo->est        = the_globals->getEST();
622	<	}
623	<	}
624	<	}
625	<
516	>	myCutoffGroup = new CutoffGroup();
517	>
518		#ifdef IS_MPI
519	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
520	<	MPIcheckPoint();
521	<	#endif // is_mpi
519	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(j + groupOffset);
522	>	#endif
523	>
524	>	for (int cg = 0; cg < nMembers; cg++) {
525
526	<	if( the_globals->haveInitialConfig() ){
527	<
528	<	InitializeFromFile* fileInit;
529	<	#ifdef IS_MPI // is_mpi
530	<	if( worldRank == 0 ){
531	<	#endif //is_mpi
637	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
526	>	// molI is atom numbering inside this molecule
527	>	molI = currentCutoffGroup->getMember(cg);
528	>
529	>	// tempI is atom numbering on local processor
530	>	tempI = molI + atomOffset;
531	>
532		#ifdef IS_MPI
533	<	}else fileInit = new InitializeFromFile( NULL );
533	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = j + groupOffset;
538		#endif
539	<	fileInit->read_xyz( simnfo ); // default velocities on
539	>
540
541	<	delete fileInit;
542	<	}
543	<	else{
541	>
542	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
543	>
544	>	cutoffAtomSet.insert(tempI);
545	>	}
546	>
547	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
548	>	groupOffset++;
549
550	<	#ifdef IS_MPI
550	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
551	>
552	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
553	>
554	>	for(j = 0; j < molInfo.nAtoms; j++){
555	>
556	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
557	>	myCutoffGroup = new CutoffGroup();
558	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
559
560	<	// no init from bass
561	<
562	<	sprintf( painCave.errMsg,
563	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
560	>	#ifdef IS_MPI
561	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
562	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
563	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
564		#else
565	+	myCutoffGroup->setGlobalIndex(j + groupOffset);
566	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
567	+	info[k].globalGroupMembership[globalID] = j+groupOffset;
568	+	#endif
569	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
570	+	groupOffset++;
571	+	}
572	+
573	+	}
574
575	<	initFromBass();
575	>	// After this is all set up, scan through the atoms to
576	>	// see if they can be added to the integrableObjects:
577
578	+	molInfo.myIntegrableObjects.clear();
579	+
580
581	<	#endif
662	<	}
581	>	for (j = 0; j < molInfo.nAtoms; j++){
582
583		#ifdef IS_MPI
584	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
585	<	MPIcheckPoint();
586	<	#endif // is_mpi
584	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
585	>	#else
586	>	slJ = j+atomOffset;
587	>	#endif
588
589	+	// if they aren't on the skip list, then they can be integrated
590
591	<
592	<
593	<
591	>	if (skipList.find(slJ) == skipList.end()) {
592	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
593	>	info[k].integrableObjects.push_back(mySD);
594	>	molInfo.myIntegrableObjects.push_back(mySD);
595	>	}
596	>	}
597
598	<
599	<	#ifdef IS_MPI
600	<	if( worldRank == 0 ){
601	<	#endif // is_mpi
602	<
603	<	if( the_globals->haveFinalConfig() ){
680	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
681	<	}
682	<	else{
683	<	strcpy( simnfo->finalName, inFileName );
684	<	char* endTest;
685	<	int nameLength = strlen( simnfo->finalName );
686	<	endTest = &(simnfo->finalName[nameLength - 5]);
687	<	if( !strcmp( endTest, ".bass" ) ){
688	<	strcpy( endTest, ".eor" );
598	>	// all rigid bodies are integrated:
599	>
600	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
601	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
602	>	info[k].integrableObjects.push_back(mySD);
603	>	molInfo.myIntegrableObjects.push_back(mySD);
604		}
605	<	else if( !strcmp( endTest, ".BASS" ) ){
606	<	strcpy( endTest, ".eor" );
607	<	}
608	<	else{
609	<	endTest = &(simnfo->finalName[nameLength - 4]);
610	<	if( !strcmp( endTest, ".bss" ) ){
611	<	strcpy( endTest, ".eor" );
612	<	}
613	<	else if( !strcmp( endTest, ".mdl" ) ){
614	<	strcpy( endTest, ".eor" );
615	<	}
616	<	else{
617	<	strcat( simnfo->finalName, ".eor" );
618	<	}
619	<	}
620	<	}
621	<
622	<	// make the sample and status out names
623	<
624	<	strcpy( simnfo->sampleName, inFileName );
625	<	char* endTest;
626	<	int nameLength = strlen( simnfo->sampleName );
627	<	endTest = &(simnfo->sampleName[nameLength - 5]);
628	<	if( !strcmp( endTest, ".bass" ) ){
629	<	strcpy( endTest, ".dump" );
630	<	}
631	<	else if( !strcmp( endTest, ".BASS" ) ){
632	<	strcpy( endTest, ".dump" );
633	<	}
634	<	else{
635	<	endTest = &(simnfo->sampleName[nameLength - 4]);
636	<	if( !strcmp( endTest, ".bss" ) ){
637	<	strcpy( endTest, ".dump" );
638	<	}
639	<	else if( !strcmp( endTest, ".mdl" ) ){
640	<	strcpy( endTest, ".dump" );
641	<	}
642	<	else{
643	<	strcat( simnfo->sampleName, ".dump" );
644	<	}
645	<	}
646	<
647	<	strcpy( simnfo->statusName, inFileName );
648	<	nameLength = strlen( simnfo->statusName );
649	<	endTest = &(simnfo->statusName[nameLength - 5]);
650	<	if( !strcmp( endTest, ".bass" ) ){
651	<	strcpy( endTest, ".stat" );
652	<	}
653	<	else if( !strcmp( endTest, ".BASS" ) ){
654	<	strcpy( endTest, ".stat" );
655	<	}
656	<	else{
657	<	endTest = &(simnfo->statusName[nameLength - 4]);
658	<	if( !strcmp( endTest, ".bss" ) ){
659	<	strcpy( endTest, ".stat" );
660	<	}
661	<	else if( !strcmp( endTest, ".mdl" ) ){
662	<	strcpy( endTest, ".stat" );
663	<	}
664	<	else{
665	<	strcat( simnfo->statusName, ".stat" );
666	<	}
667	<	}
668	<
669	<	#ifdef IS_MPI
670	<	}
671	<	#endif // is_mpi
672	<
673	<	// set the status, sample, and themal kick times
674	<
675	<	if( the_globals->haveSampleTime() ){
676	<	simnfo->sampleTime = the_globals->getSampleTime();
677	<	simnfo->statusTime = simnfo->sampleTime;
678	<	simnfo->thermalTime = simnfo->sampleTime;
679	<	}
680	<	else{
681	<	simnfo->sampleTime = the_globals->getRunTime();
682	<	simnfo->statusTime = simnfo->sampleTime;
683	<	simnfo->thermalTime = simnfo->sampleTime;
684	<	}
685	<
686	<	if( the_globals->haveStatusTime() ){
687	<	simnfo->statusTime = the_globals->getStatusTime();
688	<	}
689	<
690	<	if( the_globals->haveThermalTime() ){
691	<	simnfo->thermalTime = the_globals->getThermalTime();
692	<	}
693	<
694	<	// check for the temperature set flag
695	<
696	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
697	<
698	<
699	<	// make the integrator
700	<
701	<
702	<	NVT*  myNVT = NULL;
703	<	NPTi* myNPTi = NULL;
704	<	NPTf* myNPTf = NULL;
705	<	NPTim* myNPTim = NULL;
706	<
707	<	switch( ensembleCase ){
708	<
709	<	case NVE_ENS:
710	<	new NVE( simnfo, the_ff );
711	<	break;
712	<
713	<	case NVT_ENS:
714	<	myNVT = new NVT( simnfo, the_ff );
715	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
716	<
717	<	if (the_globals->haveTauThermostat())
718	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
719	<
720	<	else {
721	<	sprintf( painCave.errMsg,
722	<	"SimSetup error: If you use the NVT\n"
723	<	"    ensemble, you must set tauThermostat.\n");
724	<	painCave.isFatal = 1;
725	<	simError();
726	<	}
727	<	break;
728	<
729	<	case NPTi_ENS:
730	<	myNPTi = new NPTi( simnfo, the_ff );
731	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
732	<
733	<	if (the_globals->haveTargetPressure())
734	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
735	<	else {
736	<	sprintf( painCave.errMsg,
737	<	"SimSetup error: If you use a constant pressure\n"
738	<	"    ensemble, you must set targetPressure in the BASS file.\n");
739	<	painCave.isFatal = 1;
740	<	simError();
741	<	}
742	<
743	<	if( the_globals->haveTauThermostat() )
744	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
745	<	else{
746	<	sprintf( painCave.errMsg,
747	<	"SimSetup error: If you use an NPT\n"
748	<	"    ensemble, you must set tauThermostat.\n");
749	<	painCave.isFatal = 1;
750	<	simError();
751	<	}
752	<
753	<	if( the_globals->haveTauBarostat() )
754	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
755	<	else{
756	<	sprintf( painCave.errMsg,
757	<	"SimSetup error: If you use an NPT\n"
758	<	"    ensemble, you must set tauBarostat.\n");
759	<	painCave.isFatal = 1;
760	<	simError();
761	<	}
762	<	break;
763	<
764	<	case NPTf_ENS:
765	<	myNPTf = new NPTf( simnfo, the_ff );
766	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
767	<
768	<	if (the_globals->haveTargetPressure())
769	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
770	<	else {
771	<	sprintf( painCave.errMsg,
772	<	"SimSetup error: If you use a constant pressure\n"
773	<	"    ensemble, you must set targetPressure in the BASS file.\n");
774	<	painCave.isFatal = 1;
775	<	simError();
776	<	}
777	<
778	<	if( the_globals->haveTauThermostat() )
779	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
780	<	else{
781	<	sprintf( painCave.errMsg,
782	<	"SimSetup error: If you use an NPT\n"
783	<	"    ensemble, you must set tauThermostat.\n");
784	<	painCave.isFatal = 1;
785	<	simError();
786	<	}
787	<
788	<	if( the_globals->haveTauBarostat() )
789	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
790	<	else{
791	<	sprintf( painCave.errMsg,
792	<	"SimSetup error: If you use an NPT\n"
793	<	"    ensemble, you must set tauBarostat.\n");
794	<	painCave.isFatal = 1;
795	<	simError();
796	<	}
797	<	break;
798	<
799	<	case NPTim_ENS:
800	<	myNPTim = new NPTim( simnfo, the_ff );
801	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
802	<
803	<	if (the_globals->haveTargetPressure())
804	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
805	<	else {
806	<	sprintf( painCave.errMsg,
807	<	"SimSetup error: If you use a constant pressure\n"
808	<	"    ensemble, you must set targetPressure in the BASS file.\n");
809	<	painCave.isFatal = 1;
810	<	simError();
811	<	}
812	<
813	<	if( the_globals->haveTauThermostat() )
814	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
815	<	else{
816	<	sprintf( painCave.errMsg,
817	<	"SimSetup error: If you use an NPT\n"
818	<	"    ensemble, you must set tauThermostat.\n");
819	<	painCave.isFatal = 1;
820	<	simError();
821	<	}
822	<
823	<	if( the_globals->haveTauBarostat() )
824	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
825	<	else{
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup error: If you use an NPT\n"
828	<	"    ensemble, you must set tauBarostat.\n");
829	<	painCave.isFatal = 1;
830	<	simError();
831	<	}
832	<	break;
833	<
834	<
835	<
836	<	default:
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
839	<	painCave.isFatal = 1;
840	<	simError();
841	<	}
842	<
843	<
844	<	#ifdef IS_MPI
845	<	mpiSim->mpiRefresh();
846	<	#endif
847	<
848	<	// initialize the Fortran
849	<
850	<
851	<	simnfo->refreshSim();
852	<
853	<	if( !strcmp( simnfo->mixingRule, "standard") ){
854	<	the_ff->initForceField( LB_MIXING_RULE );
855	<	}
856	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
857	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
858	<	}
859	<	else{
860	<	sprintf( painCave.errMsg,
861	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
862	<	simnfo->mixingRule );
863	<	painCave.isFatal = 1;
864	<	simError();
865	<	}
866	<
867	<
868	<	#ifdef IS_MPI
869	<	strcpy( checkPointMsg,
870	<	"Successfully intialized the mixingRule for Fortran." );
871	<	MPIcheckPoint();
872	<	#endif // is_mpi
873	<	}
874	<
875	<
876	<	void SimSetup::makeMolecules( void ){
877	<
878	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
879	<	molInit info;
880	<	DirectionalAtom* dAtom;
881	<	LinkedAssign* extras;
882	<	LinkedAssign* current_extra;
883	<	AtomStamp* currentAtom;
884	<	BondStamp* currentBond;
885	<	BendStamp* currentBend;
886	<	TorsionStamp* currentTorsion;
887	<
888	<	bond_pair* theBonds;
889	<	bend_set* theBends;
890	<	torsion_set* theTorsions;
891	<
892	<
893	<	//init the forceField paramters
894	<
895	<	the_ff->readParams();
896	<
897	<
898	<	// init the atoms
899	<
900	<	double ux, uy, uz, u, uSqr;
901	<
902	<	atomOffset = 0;
903	<	excludeOffset = 0;
904	<	for(i=0; i<simnfo->n_mol; i++){
905	<
906	<	stampID = the_molecules[i].getStampID();
907	<
908	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
909	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
910	<	info.nBends    = comp_stamps[stampID]->getNBends();
911	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
912	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
913	<
914	<	info.myAtoms = &the_atoms[atomOffset];
915	<	info.myExcludes = &the_excludes[excludeOffset];
916	<	info.myBonds = new Bond*[info.nBonds];
917	<	info.myBends = new Bend*[info.nBends];
918	<	info.myTorsions = new Torsion*[info.nTorsions];
919	<
920	<	theBonds = new bond_pair[info.nBonds];
921	<	theBends = new bend_set[info.nBends];
922	<	theTorsions = new torsion_set[info.nTorsions];
923	<
924	<	// make the Atoms
925	<
926	<	for(j=0; j<info.nAtoms; j++){
927	<
928	<	currentAtom = comp_stamps[stampID]->getAtom( j );
929	<	if( currentAtom->haveOrientation() ){
930	<
931	<	dAtom = new DirectionalAtom(j + atomOffset);
932	<	simnfo->n_oriented++;
933	<	info.myAtoms[j] = dAtom;
934	<
935	<	ux = currentAtom->getOrntX();
936	<	uy = currentAtom->getOrntY();
937	<	uz = currentAtom->getOrntZ();
938	<
939	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
940	<
941	<	u = sqrt( uSqr );
942	<	ux = ux / u;
943	<	uy = uy / u;
944	<	uz = uz / u;
945	<
946	<	dAtom->setSUx( ux );
947	<	dAtom->setSUy( uy );
948	<	dAtom->setSUz( uz );
949	<	}
950	<	else{
951	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
952	<	}
953	<	info.myAtoms[j]->setType( currentAtom->getType() );
954	<
955	<	#ifdef IS_MPI
956	<
957	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
958	<
959	<	#endif // is_mpi
960	<	}
961	<
962	<	// make the bonds
963	<	for(j=0; j<info.nBonds; j++){
964	<
965	<	currentBond = comp_stamps[stampID]->getBond( j );
966	<	theBonds[j].a = currentBond->getA() + atomOffset;
967	<	theBonds[j].b = currentBond->getB() + atomOffset;
968	<
969	<	exI = theBonds[j].a;
970	<	exJ = theBonds[j].b;
971	<
972	<	// exclude_I must always be the smaller of the pair
973	<	if( exI > exJ ){
974	<	tempEx = exI;
975	<	exI = exJ;
976	<	exJ = tempEx;
977	<	}
978	<	#ifdef IS_MPI
979	<	tempEx = exI;
980	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
981	<	tempEx = exJ;
982	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
983	<
984	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
985	<	#else  // isn't MPI
986	<
987	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
988	<	#endif  //is_mpi
989	<	}
990	<	excludeOffset += info.nBonds;
991	<
992	<	//make the bends
993	<	for(j=0; j<info.nBends; j++){
994	<
995	<	currentBend = comp_stamps[stampID]->getBend( j );
996	<	theBends[j].a = currentBend->getA() + atomOffset;
997	<	theBends[j].b = currentBend->getB() + atomOffset;
998	<	theBends[j].c = currentBend->getC() + atomOffset;
999	<
1000	<	if( currentBend->haveExtras() ){
1001	<
1002	<	extras = currentBend->getExtras();
1003	<	current_extra = extras;
1004	<
1005	<	while( current_extra != NULL ){
1006	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1007	<
1008	<	switch( current_extra->getType() ){
1009	<
1010	<	case 0:
1011	<	theBends[j].ghost =
1012	<	current_extra->getInt() + atomOffset;
1013	<	theBends[j].isGhost = 1;
1014	<	break;
1015	<
1016	<	case 1:
1017	<	theBends[j].ghost =
1018	<	(int)current_extra->getDouble() + atomOffset;
1019	<	theBends[j].isGhost = 1;
1020	<	break;
1021	<
1022	<	default:
1023	<	sprintf( painCave.errMsg,
1024	<	"SimSetup Error: ghostVectorSource was neither a "
1025	<	"double nor an int.\n"
1026	<	"-->Bend[%d] in %s\n",
1027	<	j, comp_stamps[stampID]->getID() );
1028	<	painCave.isFatal = 1;
1029	<	simError();
1030	<	}
1031	<	}
1032	<
1033	<	else{
1034	<
1035	<	sprintf( painCave.errMsg,
1036	<	"SimSetup Error: unhandled bend assignment:\n"
1037	<	"    -->%s in Bend[%d] in %s\n",
1038	<	current_extra->getlhs(),
1039	<	j, comp_stamps[stampID]->getID() );
1040	<	painCave.isFatal = 1;
1041	<	simError();
1042	<	}
1043	<
1044	<	current_extra = current_extra->getNext();
1045	<	}
1046	<	}
1047	<
1048	<	if( !theBends[j].isGhost ){
1049	<
1050	<	exI = theBends[j].a;
1051	<	exJ = theBends[j].c;
1052	<	}
1053	<	else{
1054	<
1055	<	exI = theBends[j].a;
1056	<	exJ = theBends[j].b;
1057	<	}
1058	<
1059	<	// exclude_I must always be the smaller of the pair
1060	<	if( exI > exJ ){
1061	<	tempEx = exI;
1062	<	exI = exJ;
1063	<	exJ = tempEx;
1064	<	}
1065	<	#ifdef IS_MPI
1066	<	tempEx = exI;
1067	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	<	tempEx = exJ;
1069	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1070	<
1071	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1072	<	#else  // isn't MPI
1073	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1074	<	#endif  //is_mpi
1075	<	}
1076	<	excludeOffset += info.nBends;
1077	<
1078	<	for(j=0; j<info.nTorsions; j++){
1079	<
1080	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1081	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1082	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1083	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1084	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1085	<
1086	<	exI = theTorsions[j].a;
1087	<	exJ = theTorsions[j].d;
1088	<
1089	<	// exclude_I must always be the smaller of the pair
1090	<	if( exI > exJ ){
1091	<	tempEx = exI;
1092	<	exI = exJ;
1093	<	exJ = tempEx;
1094	<	}
1095	<	#ifdef IS_MPI
1096	<	tempEx = exI;
1097	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1098	<	tempEx = exJ;
1099	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1100	<
1101	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1102	<	#else  // isn't MPI
1103	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1104	<	#endif  //is_mpi
1105	<	}
1106	<	excludeOffset += info.nTorsions;
1107	<
1108	<
1109	<	// send the arrays off to the forceField for init.
1110	<
1111	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1112	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1113	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1114	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1115	<
1116	<
1117	<	the_molecules[i].initialize( info );
1118	<
1119	<
1120	<	atomOffset += info.nAtoms;
1121	<	delete[] theBonds;
1122	<	delete[] theBends;
1123	<	delete[] theTorsions;
1124	<	}
1125	<
1126	<	#ifdef IS_MPI
1127	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1128	<	MPIcheckPoint();
1129	<	#endif // is_mpi
1130	<
1131	<	// clean up the forcefield
1132	<	the_ff->calcRcut();
1133	<	the_ff->cleanMe();
1134	<
1135	<	}
1136	<
1137	<	void SimSetup::initFromBass( void ){
1138	<
1139	<	int i, j, k;
1140	<	int n_cells;
1141	<	double cellx, celly, cellz;
1142	<	double temp1, temp2, temp3;
1143	<	int n_per_extra;
1144	<	int n_extra;
1145	<	int have_extra, done;
1146	<
1147	<	temp1 = (double)tot_nmol / 4.0;
1148	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1149	<	temp3 = ceil( temp2 );
1150	<
1151	<	have_extra =0;
1152	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1153	<	have_extra =1;
1154	<
1155	<	n_cells = (int)temp3 - 1;
1156	<	cellx = simnfo->boxLx / temp3;
1157	<	celly = simnfo->boxLy / temp3;
1158	<	cellz = simnfo->boxLz / temp3;
1159	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1160	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1161	<	n_per_extra = (int)ceil( temp1 );
1162	<
1163	<	if( n_per_extra > 4){
1164	<	sprintf( painCave.errMsg,
1165	<	"SimSetup error. There has been an error in constructing"
1166	<	" the non-complete lattice.\n" );
1167	<	painCave.isFatal = 1;
1168	<	simError();
1169	<	}
1170	<	}
1171	<	else{
1172	<	n_cells = (int)temp3;
1173	<	cellx = simnfo->boxLx / temp3;
1174	<	celly = simnfo->boxLy / temp3;
1175	<	cellz = simnfo->boxLz / temp3;
1176	<	}
1177	<
1178	<	current_mol = 0;
1179	<	current_comp_mol = 0;
1180	<	current_comp = 0;
1181	<	current_atom_ndx = 0;
1182	<
1183	<	for( i=0; i < n_cells ; i++ ){
1184	<	for( j=0; j < n_cells; j++ ){
1185	<	for( k=0; k < n_cells; k++ ){
1186	<
1187	<	makeElement( i * cellx,
1188	<	j * celly,
1189	<	k * cellz );
1190	<
1191	<	makeElement( i * cellx + 0.5 * cellx,
1192	<	j * celly + 0.5 * celly,
1193	<	k * cellz );
1194	<
1195	<	makeElement( i * cellx,
1196	<	j * celly + 0.5 * celly,
1197	<	k * cellz + 0.5 * cellz );
1198	<
1199	<	makeElement( i * cellx + 0.5 * cellx,
1200	<	j * celly,
1201	<	k * cellz + 0.5 * cellz );
1202	<	}
1203	<	}
1204	<	}
1205	<
1206	<	if( have_extra ){
1207	<	done = 0;
1208	<
1209	<	int start_ndx;
1210	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1211	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1212	<
1213	<	if( i < n_cells ){
1214	<
1215	<	if( j < n_cells ){
1216	<	start_ndx = n_cells;
1217	<	}
1218	<	else start_ndx = 0;
1219	<	}
1220	<	else start_ndx = 0;
1221	<
1222	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1223	<
1224	<	makeElement( i * cellx,
1225	<	j * celly,
1226	<	k * cellz );
1227	<	done = ( current_mol >= tot_nmol );
1228	<
1229	<	if( !done && n_per_extra > 1 ){
1230	<	makeElement( i * cellx + 0.5 * cellx,
1231	<	j * celly + 0.5 * celly,
1232	<	k * cellz );
1233	<	done = ( current_mol >= tot_nmol );
1234	<	}
1235	<
1236	<	if( !done && n_per_extra > 2){
1237	<	makeElement( i * cellx,
1238	<	j * celly + 0.5 * celly,
1239	<	k * cellz + 0.5 * cellz );
1240	<	done = ( current_mol >= tot_nmol );
1241	<	}
1242	<
1243	<	if( !done && n_per_extra > 3){
1244	<	makeElement( i * cellx + 0.5 * cellx,
1245	<	j * celly,
1246	<	k * cellz + 0.5 * cellz );
1247	<	done = ( current_mol >= tot_nmol );
1248	<	}
1249	<	}
1250	<	}
1251	<	}
1252	<	}
1253	<
1254	<
1255	<	for( i=0; i<simnfo->n_atoms; i++ ){
1256	<	simnfo->atoms[i]->set_vx( 0.0 );
1257	<	simnfo->atoms[i]->set_vy( 0.0 );
1258	<	simnfo->atoms[i]->set_vz( 0.0 );
1259	<	}
1260	<	}
1261	<
1262	<	void SimSetup::makeElement( double x, double y, double z ){
1263	<
1264	<	int k;
1265	<	AtomStamp* current_atom;
1266	<	DirectionalAtom* dAtom;
1267	<	double rotMat[3][3];
1268	<
1269	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1270	<
1271	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1272	<	if( !current_atom->havePosition() ){
1273	<	sprintf( painCave.errMsg,
1274	<	"SimSetup:initFromBass error.\n"
1275	<	"\tComponent %s, atom %s does not have a position specified.\n"
1276	<	"\tThe initialization routine is unable to give a start"
1277	<	" position.\n",
1278	<	comp_stamps[current_comp]->getID(),
1279	<	current_atom->getType() );
1280	<	painCave.isFatal = 1;
1281	<	simError();
1282	<	}
1283	<
1284	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1285	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1286	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1287	<
1288	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1289	<
1290	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1291	<
1292	<	rotMat[0][0] = 1.0;
1293	<	rotMat[0][1] = 0.0;
1294	<	rotMat[0][2] = 0.0;
1295	<
1296	<	rotMat[1][0] = 0.0;
1297	<	rotMat[1][1] = 1.0;
1298	<	rotMat[1][2] = 0.0;
1299	<
1300	<	rotMat[2][0] = 0.0;
1301	<	rotMat[2][1] = 0.0;
1302	<	rotMat[2][2] = 1.0;
1303	<
1304	<	dAtom->setA( rotMat );
1305	<	}
1306	<
1307	<	current_atom_ndx++;
1308	<	}
1309	<
1310	<	current_mol++;
1311	<	current_comp_mol++;
1312	<
1313	<	if( current_comp_mol >= components_nmol[current_comp] ){
1314	<
1315	<	current_comp_mol = 0;
1316	<	current_comp++;
1317	<	}
605	>
606	>
607	>	/*
608	>
609	>	//creat ConstraintPair.
610	>	molInfo.myConstraintPair.clear();
611	>
612	>	for (j = 0; j < molInfo.nBonds; j++){
613	>
614	>	//if both atoms are in the same rigid body, just skip it
615	>	currentBond = comp_stamps[stampID]->getBond(j);
616	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
617	>
618	>	tempI = currentBond->getA() + atomOffset;
619	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
620	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
621	>	else
622	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
623	>
624	>	tempJ =  currentBond->getB() + atomOffset;
625	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
626	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
627	>	else
628	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
629	>
630	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
631	>	molInfo.myConstraintPairs.push_back(consPair);
632	>	}
633	>	}
634	>
635	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
636	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
637	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
638	>
639	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
640	>
641	>	for(size_t m = 0; m < jointAtoms.size(); m++){
642	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
643	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
644	>
645	>	consPair = new JointConstraintPair(consElement1, consElement2);
646	>	molInfo.myConstraintPairs.push_back(consPair);
647	>	}
648	>
649	>	}
650	>	}
651	>
652	>	*/
653	>	// send the arrays off to the forceField for init.
654	>
655	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
656	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
657	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
658	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
659	>	theTorsions);
660	>
661	>	info[k].molecules[i].initialize(molInfo);
662	>
663	>
664	>	atomOffset += molInfo.nAtoms;
665	>	delete[] theBonds;
666	>	delete[] theBends;
667	>	delete[] theTorsions;
668	>	}
669	>
670	>
671	>
672	>	#ifdef IS_MPI
673	>	// Since the globalGroupMembership has been zero filled and we've only
674	>	// poked values into the atoms we know, we can do an Allreduce
675	>	// to get the full globalGroupMembership array (We think).
676	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
677	>	// docs said we could.
678	>
679	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
680	>
681	>	MPI_Allreduce(info[k].globalGroupMembership,
682	>	ggMjunk,
683	>	mpiSim->getNAtomsGlobal(),
684	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
685	>
686	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
687	>	info[k].globalGroupMembership[i] = ggMjunk[i];
688	>
689	>	delete[] ggMjunk;
690	>
691	>	#endif
692	>
693	>
694	>
695	>	}
696	>
697	>	#ifdef IS_MPI
698	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
699	>	MPIcheckPoint();
700	>	#endif // is_mpi
701	>
702	>	}
703	>
704	>	void SimSetup::initFromBass(void){
705	>	int i, j, k;
706	>	int n_cells;
707	>	double cellx, celly, cellz;
708	>	double temp1, temp2, temp3;
709	>	int n_per_extra;
710	>	int n_extra;
711	>	int have_extra, done;
712	>
713	>	double vel[3];
714	>	vel[0] = 0.0;
715	>	vel[1] = 0.0;
716	>	vel[2] = 0.0;
717	>
718	>	temp1 = (double) tot_nmol / 4.0;
719	>	temp2 = pow(temp1, (1.0 / 3.0));
720	>	temp3 = ceil(temp2);
721	>
722	>	have_extra = 0;
723	>	if (temp2 < temp3){
724	>	// we have a non-complete lattice
725	>	have_extra = 1;
726	>
727	>	n_cells = (int) temp3 - 1;
728	>	cellx = info[0].boxL[0] / temp3;
729	>	celly = info[0].boxL[1] / temp3;
730	>	cellz = info[0].boxL[2] / temp3;
731	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
732	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
733	>	n_per_extra = (int) ceil(temp1);
734	>
735	>	if (n_per_extra > 4){
736	>	sprintf(painCave.errMsg,
737	>	"SimSetup error. There has been an error in constructing"
738	>	" the non-complete lattice.\n");
739	>	painCave.isFatal = 1;
740	>	simError();
741	>	}
742	>	}
743	>	else{
744	>	n_cells = (int) temp3;
745	>	cellx = info[0].boxL[0] / temp3;
746	>	celly = info[0].boxL[1] / temp3;
747	>	cellz = info[0].boxL[2] / temp3;
748	>	}
749	>
750	>	current_mol = 0;
751	>	current_comp_mol = 0;
752	>	current_comp = 0;
753	>	current_atom_ndx = 0;
754	>
755	>	for (i = 0; i < n_cells ; i++){
756	>	for (j = 0; j < n_cells; j++){
757	>	for (k = 0; k < n_cells; k++){
758	>	makeElement(i * cellx, j * celly, k * cellz);
759	>
760	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
761	>
762	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
763	>
764	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
765	>	}
766	>	}
767	>	}
768	>
769	>	if (have_extra){
770	>	done = 0;
771	>
772	>	int start_ndx;
773	>	for (i = 0; i < (n_cells + 1) && !done; i++){
774	>	for (j = 0; j < (n_cells + 1) && !done; j++){
775	>	if (i < n_cells){
776	>	if (j < n_cells){
777	>	start_ndx = n_cells;
778	>	}
779	>	else
780	>	start_ndx = 0;
781	>	}
782	>	else
783	>	start_ndx = 0;
784	>
785	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
786	>	makeElement(i * cellx, j * celly, k * cellz);
787	>	done = (current_mol >= tot_nmol);
788	>
789	>	if (!done && n_per_extra > 1){
790	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
791	>	k * cellz);
792	>	done = (current_mol >= tot_nmol);
793	>	}
794	>
795	>	if (!done && n_per_extra > 2){
796	>	makeElement(i * cellx, j * celly + 0.5 * celly,
797	>	k * cellz + 0.5 * cellz);
798	>	done = (current_mol >= tot_nmol);
799	>	}
800	>
801	>	if (!done && n_per_extra > 3){
802	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
803	>	k * cellz + 0.5 * cellz);
804	>	done = (current_mol >= tot_nmol);
805	>	}
806	>	}
807	>	}
808	>	}
809	>	}
810	>
811	>	for (i = 0; i < info[0].n_atoms; i++){
812	>	info[0].atoms[i]->setVel(vel);
813	>	}
814	>	}
815	>
816	>	void SimSetup::makeElement(double x, double y, double z){
817	>	int k;
818	>	AtomStamp* current_atom;
819	>	DirectionalAtom* dAtom;
820	>	double rotMat[3][3];
821	>	double pos[3];
822	>
823	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
824	>	current_atom = comp_stamps[current_comp]->getAtom(k);
825	>	if (!current_atom->havePosition()){
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup:initFromBass error.\n"
828	>	"\tComponent %s, atom %s does not have a position specified.\n"
829	>	"\tThe initialization routine is unable to give a start"
830	>	" position.\n",
831	>	comp_stamps[current_comp]->getID(), current_atom->getType());
832	>	painCave.isFatal = 1;
833	>	simError();
834	>	}
835	>
836	>	pos[0] = x + current_atom->getPosX();
837	>	pos[1] = y + current_atom->getPosY();
838	>	pos[2] = z + current_atom->getPosZ();
839	>
840	>	info[0].atoms[current_atom_ndx]->setPos(pos);
841	>
842	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
843	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
844	>
845	>	rotMat[0][0] = 1.0;
846	>	rotMat[0][1] = 0.0;
847	>	rotMat[0][2] = 0.0;
848	>
849	>	rotMat[1][0] = 0.0;
850	>	rotMat[1][1] = 1.0;
851	>	rotMat[1][2] = 0.0;
852	>
853	>	rotMat[2][0] = 0.0;
854	>	rotMat[2][1] = 0.0;
855	>	rotMat[2][2] = 1.0;
856	>
857	>	dAtom->setA(rotMat);
858	>	}
859	>
860	>	current_atom_ndx++;
861	>	}
862	>
863	>	current_mol++;
864	>	current_comp_mol++;
865	>
866	>	if (current_comp_mol >= components_nmol[current_comp]){
867	>	current_comp_mol = 0;
868	>	current_comp++;
869	>	}
870	>	}
871	>
872	>
873	>	void SimSetup::gatherInfo(void){
874	>	int i;
875	>
876	>	ensembleCase = -1;
877	>	ffCase = -1;
878	>
879	>	// set the easy ones first
880	>
881	>	for (i = 0; i < nInfo; i++){
882	>	info[i].target_temp = globals->getTargetTemp();
883	>	info[i].dt = globals->getDt();
884	>	info[i].run_time = globals->getRunTime();
885	>	}
886	>	n_components = globals->getNComponents();
887	>
888	>
889	>	// get the forceField
890	>
891	>	strcpy(force_field, globals->getForceField());
892	>
893	>	if (!strcasecmp(force_field, "DUFF")){
894	>	ffCase = FF_DUFF;
895	>	}
896	>	else if (!strcasecmp(force_field, "LJ")){
897	>	ffCase = FF_LJ;
898	>	}
899	>	else if (!strcasecmp(force_field, "EAM")){
900	>	ffCase = FF_EAM;
901	>	}
902	>	else if (!strcasecmp(force_field, "WATER")){
903	>	ffCase = FF_H2O;
904	>	}
905	>	else{
906	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
907	>	force_field);
908	>	painCave.isFatal = 1;
909	>	simError();
910	>	}
911	>
912	>	// get the ensemble
913	>
914	>	strcpy(ensemble, globals->getEnsemble());
915	>
916	>	if (!strcasecmp(ensemble, "NVE")){
917	>	ensembleCase = NVE_ENS;
918	>	}
919	>	else if (!strcasecmp(ensemble, "NVT")){
920	>	ensembleCase = NVT_ENS;
921	>	}
922	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
923	>	ensembleCase = NPTi_ENS;
924	>	}
925	>	else if (!strcasecmp(ensemble, "NPTf")){
926	>	ensembleCase = NPTf_ENS;
927	>	}
928	>	else if (!strcasecmp(ensemble, "NPTxyz")){
929	>	ensembleCase = NPTxyz_ENS;
930	>	}
931	>	else{
932	>	sprintf(painCave.errMsg,
933	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
934	>	"\treverting to NVE for this simulation.\n",
935	>	ensemble);
936	>	painCave.isFatal = 0;
937	>	simError();
938	>	strcpy(ensemble, "NVE");
939	>	ensembleCase = NVE_ENS;
940	>	}
941	>
942	>	for (i = 0; i < nInfo; i++){
943	>	strcpy(info[i].ensemble, ensemble);
944	>
945	>	// get the mixing rule
946	>
947	>	strcpy(info[i].mixingRule, globals->getMixingRule());
948	>	info[i].usePBC = globals->getPBC();
949	>	}
950	>
951	>	// get the components and calculate the tot_nMol and indvidual n_mol
952	>
953	>	the_components = globals->getComponents();
954	>	components_nmol = new int[n_components];
955	>
956	>
957	>	if (!globals->haveNMol()){
958	>	// we don't have the total number of molecules, so we assume it is
959	>	// given in each component
960	>
961	>	tot_nmol = 0;
962	>	for (i = 0; i < n_components; i++){
963	>	if (!the_components[i]->haveNMol()){
964	>	// we have a problem
965	>	sprintf(painCave.errMsg,
966	>	"SimSetup Error. No global NMol or component NMol given.\n"
967	>	"\tCannot calculate the number of atoms.\n");
968	>	painCave.isFatal = 1;
969	>	simError();
970	>	}
971	>
972	>	tot_nmol += the_components[i]->getNMol();
973	>	components_nmol[i] = the_components[i]->getNMol();
974	>	}
975	>	}
976	>	else{
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup error.\n"
979	>	"\tSorry, the ability to specify total"
980	>	" nMols and then give molfractions in the components\n"
981	>	"\tis not currently supported."
982	>	" Please give nMol in the components.\n");
983	>	painCave.isFatal = 1;
984	>	simError();
985	>	}
986	>
987	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
988	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
989	>	sprintf(painCave.errMsg,
990	>	"Sample time is not divisible by dt.\n"
991	>	"\tThis will result in samples that are not uniformly\n"
992	>	"\tdistributed in time.  If this is a problem, change\n"
993	>	"\tyour sampleTime variable.\n");
994	>	painCave.isFatal = 0;
995	>	simError();
996	>	}
997	>
998	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
999	>	sprintf(painCave.errMsg,
1000	>	"Status time is not divisible by dt.\n"
1001	>	"\tThis will result in status reports that are not uniformly\n"
1002	>	"\tdistributed in time.  If this is a problem, change \n"
1003	>	"\tyour statusTime variable.\n");
1004	>	painCave.isFatal = 0;
1005	>	simError();
1006	>	}
1007	>
1008	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1009	>	sprintf(painCave.errMsg,
1010	>	"Thermal time is not divisible by dt.\n"
1011	>	"\tThis will result in thermalizations that are not uniformly\n"
1012	>	"\tdistributed in time.  If this is a problem, change \n"
1013	>	"\tyour thermalTime variable.\n");
1014	>	painCave.isFatal = 0;
1015	>	simError();
1016	>	}
1017	>
1018	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1019	>	sprintf(painCave.errMsg,
1020	>	"Reset time is not divisible by dt.\n"
1021	>	"\tThis will result in integrator resets that are not uniformly\n"
1022	>	"\tdistributed in time.  If this is a problem, change\n"
1023	>	"\tyour resetTime variable.\n");
1024	>	painCave.isFatal = 0;
1025	>	simError();
1026	>	}
1027	>
1028	>	// set the status, sample, and thermal kick times
1029	>
1030	>	for (i = 0; i < nInfo; i++){
1031	>	if (globals->haveSampleTime()){
1032	>	info[i].sampleTime = globals->getSampleTime();
1033	>	info[i].statusTime = info[i].sampleTime;
1034	>	}
1035	>	else{
1036	>	info[i].sampleTime = globals->getRunTime();
1037	>	info[i].statusTime = info[i].sampleTime;
1038	>	}
1039	>
1040	>	if (globals->haveStatusTime()){
1041	>	info[i].statusTime = globals->getStatusTime();
1042	>	}
1043	>
1044	>	if (globals->haveThermalTime()){
1045	>	info[i].thermalTime = globals->getThermalTime();
1046	>	} else {
1047	>	info[i].thermalTime = globals->getRunTime();
1048	>	}
1049	>
1050	>	info[i].resetIntegrator = 0;
1051	>	if( globals->haveResetTime() ){
1052	>	info[i].resetTime = globals->getResetTime();
1053	>	info[i].resetIntegrator = 1;
1054	>	}
1055	>
1056	>	// check for the temperature set flag
1057	>
1058	>	if (globals->haveTempSet())
1059	>	info[i].setTemp = globals->getTempSet();
1060	>
1061	>	// check for the extended State init
1062	>
1063	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1064	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065	>
1066	>	// check for thermodynamic integration
1067	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1068	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1069	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1070	>	info[i].thermIntLambda = globals->getThermIntLambda();
1071	>	info[i].thermIntK = globals->getThermIntK();
1072	>
1073	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1074	>	info[i].restraint = myRestraint;
1075	>	}
1076	>	else {
1077	>	sprintf(painCave.errMsg,
1078	>	"SimSetup Error:\n"
1079	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1080	>	"\tthermodynamicIntegrationLambda (and/or\n"
1081	>	"\tthermodynamicIntegrationK) was not specified.\n"
1082	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1083	>	painCave.isFatal = 1;
1084	>	simError();
1085	>	}
1086	>	}
1087	>	else if(globals->getUseLiquidThermInt()) {
1088	>	if (globals->getUseSolidThermInt()) {
1089	>	sprintf( painCave.errMsg,
1090	>	"SimSetup Warning: It appears that you have both solid and\n"
1091	>	"\tliquid thermodynamic integration activated in your .bass\n"
1092	>	"\tfile. To avoid confusion, specify only one technique in\n"
1093	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1094	>	"\twill be assumed for the current simulation. If this is not\n"
1095	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1096	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1097	>	painCave.isFatal = 0;
1098	>	simError();
1099	>	}
1100	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1101	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1102	>	info[i].thermIntLambda = globals->getThermIntLambda();
1103	>	info[i].thermIntK = globals->getThermIntK();
1104	>	}
1105	>	else {
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error:\n"
1108	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1109	>	"\tthermodynamicIntegrationLambda (and/or\n"
1110	>	"\tthermodynamicIntegrationK) was not specified.\n"
1111	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1112	>	painCave.isFatal = 1;
1113	>	simError();
1114	>	}
1115	>	}
1116	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1117	>	sprintf(painCave.errMsg,
1118	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1119	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1120	>	"\t'true' in your .bass file.  These keywords are set to\n"
1121	>	"\t'false' by default, so your lambda and/or k values are\n"
1122	>	"\tbeing ignored.\n");
1123	>	painCave.isFatal = 0;
1124	>	simError();
1125	>	}
1126	>	}
1127	>
1128	>	//setup seed for random number generator
1129	>	int seedValue;
1130	>
1131	>	if (globals->haveSeed()){
1132	>	seedValue = globals->getSeed();
1133	>
1134	>	if(seedValue / 1E9 == 0){
1135	>	sprintf(painCave.errMsg,
1136	>	"Seed for sprng library should contain at least 9 digits\n"
1137	>	"OOPSE will generate a seed for user\n");
1138	>	painCave.isFatal = 0;
1139	>	simError();
1140	>
1141	>	//using seed generated by system instead of invalid seed set by user
1142	>	#ifndef IS_MPI
1143	>	seedValue = make_sprng_seed();
1144	>	#else
1145	>	if (worldRank == 0){
1146	>	seedValue = make_sprng_seed();
1147	>	}
1148	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1149	>	#endif
1150	>	}
1151	>	}//end of if branch of globals->haveSeed()
1152	>	else{
1153	>
1154	>	#ifndef IS_MPI
1155	>	seedValue = make_sprng_seed();
1156	>	#else
1157	>	if (worldRank == 0){
1158	>	seedValue = make_sprng_seed();
1159	>	}
1160	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	>	#endif
1162	>	}//end of globals->haveSeed()
1163	>
1164	>	for (int i = 0; i < nInfo; i++){
1165	>	info[i].setSeed(seedValue);
1166	>	}
1167	>
1168	>	#ifdef IS_MPI
1169	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1170	>	MPIcheckPoint();
1171	>	#endif // is_mpi
1172	>	}
1173	>
1174	>
1175	>	void SimSetup::finalInfoCheck(void){
1176	>	int index;
1177	>	int usesDipoles;
1178	>	int usesCharges;
1179	>	int i;
1180	>
1181	>	for (i = 0; i < nInfo; i++){
1182	>	// check electrostatic parameters
1183	>
1184	>	index = 0;
1185	>	usesDipoles = 0;
1186	>	while ((index < info[i].n_atoms) && !usesDipoles){
1187	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1188	>	index++;
1189	>	}
1190	>	index = 0;
1191	>	usesCharges = 0;
1192	>	while ((index < info[i].n_atoms) && !usesCharges){
1193	>	usesCharges= (info[i].atoms[index])->hasCharge();
1194	>	index++;
1195	>	}
1196	>	#ifdef IS_MPI
1197	>	int myUse = usesDipoles;
1198	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1199	>	#endif //is_mpi
1200	>
1201	>	double theRcut, theRsw;
1202	>
1203	>	if (globals->haveRcut()) {
1204	>	theRcut = globals->getRcut();
1205	>
1206	>	if (globals->haveRsw())
1207	>	theRsw = globals->getRsw();
1208	>	else
1209	>	theRsw = theRcut;
1210	>
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212	>
1213	>	} else {
1214	>
1215	>	the_ff->calcRcut();
1216	>	theRcut = info[i].getRcut();
1217	>
1218	>	if (globals->haveRsw())
1219	>	theRsw = globals->getRsw();
1220	>	else
1221	>	theRsw = theRcut;
1222	>
1223	>	info[i].setDefaultRcut(theRcut, theRsw);
1224	>	}
1225	>
1226	>	if (globals->getUseRF()){
1227	>	info[i].useReactionField = 1;
1228	>
1229	>	if (!globals->haveRcut()){
1230	>	sprintf(painCave.errMsg,
1231	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1232	>	"\tOOPSE will use a default value of 15.0 angstroms"
1233	>	"\tfor the cutoffRadius.\n");
1234	>	painCave.isFatal = 0;
1235	>	simError();
1236	>	theRcut = 15.0;
1237	>	}
1238	>	else{
1239	>	theRcut = globals->getRcut();
1240	>	}
1241	>
1242	>	if (!globals->haveRsw()){
1243	>	sprintf(painCave.errMsg,
1244	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1245	>	"\tOOPSE will use a default value of\n"
1246	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1247	>	painCave.isFatal = 0;
1248	>	simError();
1249	>	theRsw = 0.95 * theRcut;
1250	>	}
1251	>	else{
1252	>	theRsw = globals->getRsw();
1253	>	}
1254	>
1255	>	info[i].setDefaultRcut(theRcut, theRsw);
1256	>
1257	>	if (!globals->haveDielectric()){
1258	>	sprintf(painCave.errMsg,
1259	>	"SimSetup Error: No Dielectric constant was set.\n"
1260	>	"\tYou are trying to use Reaction Field without"
1261	>	"\tsetting a dielectric constant!\n");
1262	>	painCave.isFatal = 1;
1263	>	simError();
1264	>	}
1265	>	info[i].dielectric = globals->getDielectric();
1266	>	}
1267	>	else{
1268	>	if (usesDipoles || usesCharges){
1269	>
1270	>	if (!globals->haveRcut()){
1271	>	sprintf(painCave.errMsg,
1272	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1273	>	"\tOOPSE will use a default value of 15.0 angstroms"
1274	>	"\tfor the cutoffRadius.\n");
1275	>	painCave.isFatal = 0;
1276	>	simError();
1277	>	theRcut = 15.0;
1278	>	}
1279	>	else{
1280	>	theRcut = globals->getRcut();
1281	>	}
1282	>
1283	>	if (!globals->haveRsw()){
1284	>	sprintf(painCave.errMsg,
1285	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1286	>	"\tOOPSE will use a default value of\n"
1287	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1288	>	painCave.isFatal = 0;
1289	>	simError();
1290	>	theRsw = 0.95 * theRcut;
1291	>	}
1292	>	else{
1293	>	theRsw = globals->getRsw();
1294	>	}
1295	>
1296	>	info[i].setDefaultRcut(theRcut, theRsw);
1297	>
1298	>	}
1299	>	}
1300	>	}
1301	>	#ifdef IS_MPI
1302	>	strcpy(checkPointMsg, "post processing checks out");
1303	>	MPIcheckPoint();
1304	>	#endif // is_mpi
1305	>
1306	>	// clean up the forcefield
1307	>	the_ff->cleanMe();
1308	>	}
1309	>
1310	>	void SimSetup::initSystemCoords(void){
1311	>	int i;
1312	>
1313	>	char* inName;
1314	>
1315	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1316	>
1317	>	for (i = 0; i < info[0].n_atoms; i++)
1318	>	info[0].atoms[i]->setCoords();
1319	>
1320	>	if (globals->haveInitialConfig()){
1321	>	InitializeFromFile* fileInit;
1322	>	#ifdef IS_MPI // is_mpi
1323	>	if (worldRank == 0){
1324	>	#endif //is_mpi
1325	>	inName = globals->getInitialConfig();
1326	>	fileInit = new InitializeFromFile(inName);
1327	>	#ifdef IS_MPI
1328	>	}
1329	>	else
1330	>	fileInit = new InitializeFromFile(NULL);
1331	>	#endif
1332	>	fileInit->readInit(info); // default velocities on
1333	>
1334	>	delete fileInit;
1335	>	}
1336	>	else{
1337	>
1338	>	// no init from bass
1339	>
1340	>	sprintf(painCave.errMsg,
1341	>	"Cannot intialize a simulation without an initial configuration file.\n");
1342	>	painCave.isFatal = 1;;
1343	>	simError();
1344	>
1345	>	}
1346	>
1347	>	#ifdef IS_MPI
1348	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1349	>	MPIcheckPoint();
1350	>	#endif // is_mpi
1351	>	}
1352	>
1353	>
1354	>	void SimSetup::makeOutNames(void){
1355	>	int k;
1356	>
1357	>
1358	>	for (k = 0; k < nInfo; k++){
1359	>	#ifdef IS_MPI
1360	>	if (worldRank == 0){
1361	>	#endif // is_mpi
1362	>
1363	>	if (globals->haveFinalConfig()){
1364	>	strcpy(info[k].finalName, globals->getFinalConfig());
1365	>	}
1366	>	else{
1367	>	strcpy(info[k].finalName, inFileName);
1368	>	char* endTest;
1369	>	int nameLength = strlen(info[k].finalName);
1370	>	endTest = &(info[k].finalName[nameLength - 5]);
1371	>	if (!strcmp(endTest, ".bass")){
1372	>	strcpy(endTest, ".eor");
1373	>	}
1374	>	else if (!strcmp(endTest, ".BASS")){
1375	>	strcpy(endTest, ".eor");
1376	>	}
1377	>	else{
1378	>	endTest = &(info[k].finalName[nameLength - 4]);
1379	>	if (!strcmp(endTest, ".bss")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else if (!strcmp(endTest, ".mdl")){
1383	>	strcpy(endTest, ".eor");
1384	>	}
1385	>	else{
1386	>	strcat(info[k].finalName, ".eor");
1387	>	}
1388	>	}
1389	>	}
1390	>
1391	>	// make the sample and status out names
1392	>
1393	>	strcpy(info[k].sampleName, inFileName);
1394	>	char* endTest;
1395	>	int nameLength = strlen(info[k].sampleName);
1396	>	endTest = &(info[k].sampleName[nameLength - 5]);
1397	>	if (!strcmp(endTest, ".bass")){
1398	>	strcpy(endTest, ".dump");
1399	>	}
1400	>	else if (!strcmp(endTest, ".BASS")){
1401	>	strcpy(endTest, ".dump");
1402	>	}
1403	>	else{
1404	>	endTest = &(info[k].sampleName[nameLength - 4]);
1405	>	if (!strcmp(endTest, ".bss")){
1406	>	strcpy(endTest, ".dump");
1407	>	}
1408	>	else if (!strcmp(endTest, ".mdl")){
1409	>	strcpy(endTest, ".dump");
1410	>	}
1411	>	else{
1412	>	strcat(info[k].sampleName, ".dump");
1413	>	}
1414	>	}
1415	>
1416	>	strcpy(info[k].statusName, inFileName);
1417	>	nameLength = strlen(info[k].statusName);
1418	>	endTest = &(info[k].statusName[nameLength - 5]);
1419	>	if (!strcmp(endTest, ".bass")){
1420	>	strcpy(endTest, ".stat");
1421	>	}
1422	>	else if (!strcmp(endTest, ".BASS")){
1423	>	strcpy(endTest, ".stat");
1424	>	}
1425	>	else{
1426	>	endTest = &(info[k].statusName[nameLength - 4]);
1427	>	if (!strcmp(endTest, ".bss")){
1428	>	strcpy(endTest, ".stat");
1429	>	}
1430	>	else if (!strcmp(endTest, ".mdl")){
1431	>	strcpy(endTest, ".stat");
1432	>	}
1433	>	else{
1434	>	strcat(info[k].statusName, ".stat");
1435	>	}
1436	>	}
1437	>
1438	>	strcpy(info[k].rawPotName, inFileName);
1439	>	nameLength = strlen(info[k].rawPotName);
1440	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1441	>	if (!strcmp(endTest, ".bass")){
1442	>	strcpy(endTest, ".raw");
1443	>	}
1444	>	else if (!strcmp(endTest, ".BASS")){
1445	>	strcpy(endTest, ".raw");
1446	>	}
1447	>	else{
1448	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1449	>	if (!strcmp(endTest, ".bss")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else if (!strcmp(endTest, ".mdl")){
1453	>	strcpy(endTest, ".raw");
1454	>	}
1455	>	else{
1456	>	strcat(info[k].rawPotName, ".raw");
1457	>	}
1458	>	}
1459	>
1460	>	#ifdef IS_MPI
1461	>
1462	>	}
1463	>	#endif // is_mpi
1464	>	}
1465	>	}
1466	>
1467	>
1468	>	void SimSetup::sysObjectsCreation(void){
1469	>	int i, k;
1470	>
1471	>	// create the forceField
1472	>
1473	>	createFF();
1474	>
1475	>	// extract componentList
1476	>
1477	>	compList();
1478	>
1479	>	// calc the number of atoms, bond, bends, and torsions
1480	>
1481	>	calcSysValues();
1482	>
1483	>	#ifdef IS_MPI
1484	>	// divide the molecules among the processors
1485	>
1486	>	mpiMolDivide();
1487	>	#endif //is_mpi
1488	>
1489	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1490	>
1491	>	makeSysArrays();
1492	>
1493	>	// make and initialize the molecules (all but atomic coordinates)
1494	>
1495	>	makeMolecules();
1496	>
1497	>	for (k = 0; k < nInfo; k++){
1498	>	info[k].identArray = new int[info[k].n_atoms];
1499	>	for (i = 0; i < info[k].n_atoms; i++){
1500	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1501	>	}
1502	>	}
1503	>	}
1504	>
1505	>
1506	>	void SimSetup::createFF(void){
1507	>	switch (ffCase){
1508	>	case FF_DUFF:
1509	>	the_ff = new DUFF();
1510	>	break;
1511	>
1512	>	case FF_LJ:
1513	>	the_ff = new LJFF();
1514	>	break;
1515	>
1516	>	case FF_EAM:
1517	>	the_ff = new EAM_FF();
1518	>	break;
1519	>
1520	>	case FF_H2O:
1521	>	the_ff = new WATER();
1522	>	break;
1523	>
1524	>	default:
1525	>	sprintf(painCave.errMsg,
1526	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529	>	}
1530	>
1531	>	#ifdef IS_MPI
1532	>	strcpy(checkPointMsg, "ForceField creation successful");
1533	>	MPIcheckPoint();
1534	>	#endif // is_mpi
1535	>	}
1536	>
1537	>
1538	>	void SimSetup::compList(void){
1539	>	int i;
1540	>	char* id;
1541	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1542	>	LinkedMolStamp* currentStamp = NULL;
1543	>	comp_stamps = new MoleculeStamp * [n_components];
1544	>	bool haveCutoffGroups;
1545	>
1546	>	haveCutoffGroups = false;
1547	>
1548	>	// make an array of molecule stamps that match the components used.
1549	>	// also extract the used stamps out into a separate linked list
1550	>
1551	>	for (i = 0; i < nInfo; i++){
1552	>	info[i].nComponents = n_components;
1553	>	info[i].componentsNmol = components_nmol;
1554	>	info[i].compStamps = comp_stamps;
1555	>	info[i].headStamp = headStamp;
1556	>	}
1557	>
1558	>
1559	>	for (i = 0; i < n_components; i++){
1560	>	id = the_components[i]->getType();
1561	>	comp_stamps[i] = NULL;
1562	>
1563	>	// check to make sure the component isn't already in the list
1564	>
1565	>	comp_stamps[i] = headStamp->match(id);
1566	>	if (comp_stamps[i] == NULL){
1567	>	// extract the component from the list;
1568	>
1569	>	currentStamp = stamps->extractMolStamp(id);
1570	>	if (currentStamp == NULL){
1571	>	sprintf(painCave.errMsg,
1572	>	"SimSetup error: Component \"%s\" was not found in the "
1573	>	"list of declared molecules\n",
1574	>	id);
1575	>	painCave.isFatal = 1;
1576	>	simError();
1577	>	}
1578	>
1579	>	headStamp->add(currentStamp);
1580	>	comp_stamps[i] = headStamp->match(id);
1581	>	}
1582	>
1583	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1584	>	haveCutoffGroups = true;
1585	>	}
1586	>
1587	>	for (i = 0; i < nInfo; i++)
1588	>	info[i].haveCutoffGroups = haveCutoffGroups;
1589	>
1590	>	#ifdef IS_MPI
1591	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1592	>	MPIcheckPoint();
1593	>	#endif // is_mpi
1594	>	}
1595	>
1596	>	void SimSetup::calcSysValues(void){
1597	>	int i, j;
1598	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1599	>
1600	>	int* molMembershipArray;
1601	>	CutoffGroupStamp* cg;
1602	>
1603	>	tot_atoms = 0;
1604	>	tot_bonds = 0;
1605	>	tot_bends = 0;
1606	>	tot_torsions = 0;
1607	>	tot_rigid = 0;
1608	>	tot_groups = 0;
1609	>	for (i = 0; i < n_components; i++){
1610	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1611	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1612	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1613	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1614	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1615	>
1616	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1617	>	atomsingroups = 0;
1618	>	for (j=0; j < ncutgroups; j++) {
1619	>	cg = comp_stamps[i]->getCutoffGroup(j);
1620	>	atomsingroups += cg->getNMembers();
1621	>	}
1622	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1623	>	tot_groups += components_nmol[i] * ngroupsinstamp;
1624	>	}
1625	>
1626	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1627	>	molMembershipArray = new int[tot_atoms];
1628	>
1629	>	for (i = 0; i < nInfo; i++){
1630	>	info[i].n_atoms = tot_atoms;
1631	>	info[i].n_bonds = tot_bonds;
1632	>	info[i].n_bends = tot_bends;
1633	>	info[i].n_torsions = tot_torsions;
1634	>	info[i].n_SRI = tot_SRI;
1635	>	info[i].n_mol = tot_nmol;
1636	>	info[i].ngroup = tot_groups;
1637	>	info[i].molMembershipArray = molMembershipArray;
1638	>	}
1639	>	}
1640	>
1641	>	#ifdef IS_MPI
1642	>
1643	>	void SimSetup::mpiMolDivide(void){
1644	>	int i, j, k;
1645	>	int localMol, allMol;
1646	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1647	>	int local_rigid, local_groups;
1648	>	vector<int> globalMolIndex;
1649	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1650	>	CutoffGroupStamp* cg;
1651	>
1652	>	mpiSim = new mpiSimulation(info);
1653	>
1654	>	mpiSim->divideLabor();
1655	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1656	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1657	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1658	>
1659	>	// set up the local variables
1660	>
1661	>	mol2proc = mpiSim->getMolToProcMap();
1662	>	molCompType = mpiSim->getMolComponentType();
1663	>
1664	>	allMol = 0;
1665	>	localMol = 0;
1666	>	local_atoms = 0;
1667	>	local_bonds = 0;
1668	>	local_bends = 0;
1669	>	local_torsions = 0;
1670	>	local_rigid = 0;
1671	>	local_groups = 0;
1672	>	globalAtomCounter = 0;
1673	>
1674	>	for (i = 0; i < n_components; i++){
1675	>	for (j = 0; j < components_nmol[i]; j++){
1676	>	if (mol2proc[allMol] == worldRank){
1677	>	local_atoms += comp_stamps[i]->getNAtoms();
1678	>	local_bonds += comp_stamps[i]->getNBonds();
1679	>	local_bends += comp_stamps[i]->getNBends();
1680	>	local_torsions += comp_stamps[i]->getNTorsions();
1681	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1682	>
1683	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1684	>	atomsingroups = 0;
1685	>	for (k=0; k < ncutgroups; k++) {
1686	>	cg = comp_stamps[i]->getCutoffGroup(k);
1687	>	atomsingroups += cg->getNMembers();
1688	>	}
1689	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1690	>	ncutgroups;
1691	>	local_groups += ngroupsinstamp;
1692	>
1693	>	localMol++;
1694	>	}
1695	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1696	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1697	>	globalAtomCounter++;
1698	>	}
1699	>
1700	>	allMol++;
1701	>	}
1702	>	}
1703	>	local_SRI = local_bonds + local_bends + local_torsions;
1704	>
1705	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1706	>
1707	>	if (local_atoms != info[0].n_atoms){
1708	>	sprintf(painCave.errMsg,
1709	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1710	>	"\tlocalAtom (%d) are not equal.\n",
1711	>	info[0].n_atoms, local_atoms);
1712	>	painCave.isFatal = 1;
1713	>	simError();
1714	>	}
1715	>
1716	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1717	>	if (local_groups != info[0].ngroup){
1718	>	sprintf(painCave.errMsg,
1719	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1720	>	"\tlocalGroups (%d) are not equal.\n",
1721	>	info[0].ngroup, local_groups);
1722	>	painCave.isFatal = 1;
1723	>	simError();
1724	>	}
1725	>
1726	>	info[0].n_bonds = local_bonds;
1727	>	info[0].n_bends = local_bends;
1728	>	info[0].n_torsions = local_torsions;
1729	>	info[0].n_SRI = local_SRI;
1730	>	info[0].n_mol = localMol;
1731	>
1732	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1733	>	MPIcheckPoint();
1734	>	}
1735	>
1736	>	#endif // is_mpi
1737	>
1738	>
1739	>	void SimSetup::makeSysArrays(void){
1740	>
1741	>	#ifndef IS_MPI
1742	>	int k, j;
1743	>	#endif // is_mpi
1744	>	int i, l;
1745	>
1746	>	Atom** the_atoms;
1747	>	Molecule* the_molecules;
1748	>
1749	>	for (l = 0; l < nInfo; l++){
1750	>	// create the atom and short range interaction arrays
1751	>
1752	>	the_atoms = new Atom * [info[l].n_atoms];
1753	>	the_molecules = new Molecule[info[l].n_mol];
1754	>	int molIndex;
1755	>
1756	>	// initialize the molecule's stampID's
1757	>
1758	>	#ifdef IS_MPI
1759	>
1760	>
1761	>	molIndex = 0;
1762	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1763	>	if (mol2proc[i] == worldRank){
1764	>	the_molecules[molIndex].setStampID(molCompType[i]);
1765	>	the_molecules[molIndex].setMyIndex(molIndex);
1766	>	the_molecules[molIndex].setGlobalIndex(i);
1767	>	molIndex++;
1768	>	}
1769	>	}
1770	>
1771	>	#else // is_mpi
1772	>
1773	>	molIndex = 0;
1774	>	globalAtomCounter = 0;
1775	>	for (i = 0; i < n_components; i++){
1776	>	for (j = 0; j < components_nmol[i]; j++){
1777	>	the_molecules[molIndex].setStampID(i);
1778	>	the_molecules[molIndex].setMyIndex(molIndex);
1779	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1780	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1781	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1782	>	globalAtomCounter++;
1783	>	}
1784	>	molIndex++;
1785	>	}
1786	>	}
1787	>
1788	>
1789	>	#endif // is_mpi
1790	>
1791	>	info[l].globalExcludes = new int;
1792	>	info[l].globalExcludes[0] = 0;
1793	>
1794	>	// set the arrays into the SimInfo object
1795	>
1796	>	info[l].atoms = the_atoms;
1797	>	info[l].molecules = the_molecules;
1798	>	info[l].nGlobalExcludes = 0;
1799	>
1800	>	the_ff->setSimInfo(info);
1801	>	}
1802	>	}
1803	>
1804	>	void SimSetup::makeIntegrator(void){
1805	>	int k;
1806	>
1807	>	NVE<RealIntegrator>* myNVE = NULL;
1808	>	NVT<RealIntegrator>* myNVT = NULL;
1809	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1810	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1811	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1812	>
1813	>	for (k = 0; k < nInfo; k++){
1814	>	switch (ensembleCase){
1815	>	case NVE_ENS:
1816	>	if (globals->haveZconstraints()){
1817	>	setupZConstraint(info[k]);
1818	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1819	>	}
1820	>	else{
1821	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1822	>	}
1823	>
1824	>	info->the_integrator = myNVE;
1825	>	break;
1826	>
1827	>	case NVT_ENS:
1828	>	if (globals->haveZconstraints()){
1829	>	setupZConstraint(info[k]);
1830	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1831	>	}
1832	>	else
1833	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1834	>
1835	>	myNVT->setTargetTemp(globals->getTargetTemp());
1836	>
1837	>	if (globals->haveTauThermostat())
1838	>	myNVT->setTauThermostat(globals->getTauThermostat());
1839	>	else{
1840	>	sprintf(painCave.errMsg,
1841	>	"SimSetup error: If you use the NVT\n"
1842	>	"\tensemble, you must set tauThermostat.\n");
1843	>	painCave.isFatal = 1;
1844	>	simError();
1845	>	}
1846	>
1847	>	info->the_integrator = myNVT;
1848	>	break;
1849	>
1850	>	case NPTi_ENS:
1851	>	if (globals->haveZconstraints()){
1852	>	setupZConstraint(info[k]);
1853	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1854	>	}
1855	>	else
1856	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1857	>
1858	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1859	>
1860	>	if (globals->haveTargetPressure())
1861	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1862	>	else{
1863	>	sprintf(painCave.errMsg,
1864	>	"SimSetup error: If you use a constant pressure\n"
1865	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1866	>	painCave.isFatal = 1;
1867	>	simError();
1868	>	}
1869	>
1870	>	if (globals->haveTauThermostat())
1871	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1872	>	else{
1873	>	sprintf(painCave.errMsg,
1874	>	"SimSetup error: If you use an NPT\n"
1875	>	"\tensemble, you must set tauThermostat.\n");
1876	>	painCave.isFatal = 1;
1877	>	simError();
1878	>	}
1879	>
1880	>	if (globals->haveTauBarostat())
1881	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1882	>	else{
1883	>	sprintf(painCave.errMsg,
1884	>	"SimSetup error: If you use an NPT\n"
1885	>	"\tensemble, you must set tauBarostat.\n");
1886	>	painCave.isFatal = 1;
1887	>	simError();
1888	>	}
1889	>
1890	>	info->the_integrator = myNPTi;
1891	>	break;
1892	>
1893	>	case NPTf_ENS:
1894	>	if (globals->haveZconstraints()){
1895	>	setupZConstraint(info[k]);
1896	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	>	}
1898	>	else
1899	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900	>
1901	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1902	>
1903	>	if (globals->haveTargetPressure())
1904	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1905	>	else{
1906	>	sprintf(painCave.errMsg,
1907	>	"SimSetup error: If you use a constant pressure\n"
1908	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1909	>	painCave.isFatal = 1;
1910	>	simError();
1911	>	}
1912	>
1913	>	if (globals->haveTauThermostat())
1914	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1915	>
1916	>	else{
1917	>	sprintf(painCave.errMsg,
1918	>	"SimSetup error: If you use an NPT\n"
1919	>	"\tensemble, you must set tauThermostat.\n");
1920	>	painCave.isFatal = 1;
1921	>	simError();
1922	>	}
1923	>
1924	>	if (globals->haveTauBarostat())
1925	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1926	>
1927	>	else{
1928	>	sprintf(painCave.errMsg,
1929	>	"SimSetup error: If you use an NPT\n"
1930	>	"\tensemble, you must set tauBarostat.\n");
1931	>	painCave.isFatal = 1;
1932	>	simError();
1933	>	}
1934	>
1935	>	info->the_integrator = myNPTf;
1936	>	break;
1937	>
1938	>	case NPTxyz_ENS:
1939	>	if (globals->haveZconstraints()){
1940	>	setupZConstraint(info[k]);
1941	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1942	>	}
1943	>	else
1944	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1945	>
1946	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1947	>
1948	>	if (globals->haveTargetPressure())
1949	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1950	>	else{
1951	>	sprintf(painCave.errMsg,
1952	>	"SimSetup error: If you use a constant pressure\n"
1953	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1954	>	painCave.isFatal = 1;
1955	>	simError();
1956	>	}
1957	>
1958	>	if (globals->haveTauThermostat())
1959	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1960	>	else{
1961	>	sprintf(painCave.errMsg,
1962	>	"SimSetup error: If you use an NPT\n"
1963	>	"\tensemble, you must set tauThermostat.\n");
1964	>	painCave.isFatal = 1;
1965	>	simError();
1966	>	}
1967	>
1968	>	if (globals->haveTauBarostat())
1969	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1970	>	else{
1971	>	sprintf(painCave.errMsg,
1972	>	"SimSetup error: If you use an NPT\n"
1973	>	"\tensemble, you must set tauBarostat.\n");
1974	>	painCave.isFatal = 1;
1975	>	simError();
1976	>	}
1977	>
1978	>	info->the_integrator = myNPTxyz;
1979	>	break;
1980	>
1981	>	default:
1982	>	sprintf(painCave.errMsg,
1983	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1984	>	painCave.isFatal = 1;
1985	>	simError();
1986	>	}
1987	>	}
1988	>	}
1989	>
1990	>	void SimSetup::initFortran(void){
1991	>	info[0].refreshSim();
1992	>
1993	>	if (!strcmp(info[0].mixingRule, "standard")){
1994	>	the_ff->initForceField(LB_MIXING_RULE);
1995	>	}
1996	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1997	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1998	>	}
1999	>	else{
2000	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2001	>	info[0].mixingRule);
2002	>	painCave.isFatal = 1;
2003	>	simError();
2004	>	}
2005	>
2006	>
2007	>	#ifdef IS_MPI
2008	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2009	>	MPIcheckPoint();
2010	>	#endif // is_mpi
2011	>	}
2012	>
2013	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
2014	>	int nZConstraints;
2015	>	ZconStamp** zconStamp;
2016	>
2017	>	if (globals->haveZconstraintTime()){
2018	>	//add sample time of z-constraint  into SimInfo's property list
2019	>	DoubleData* zconsTimeProp = new DoubleData();
2020	>	zconsTimeProp->setID(ZCONSTIME_ID);
2021	>	zconsTimeProp->setData(globals->getZconsTime());
2022	>	theInfo.addProperty(zconsTimeProp);
2023	>	}
2024	>	else{
2025	>	sprintf(painCave.errMsg,
2026	>	"ZConstraint error: If you use a ZConstraint,\n"
2027	>	"\tyou must set zconsTime.\n");
2028	>	painCave.isFatal = 1;
2029	>	simError();
2030	>	}
2031	>
2032	>	//push zconsTol into siminfo, if user does not specify
2033	>	//value for zconsTol, a default value will be used
2034	>	DoubleData* zconsTol = new DoubleData();
2035	>	zconsTol->setID(ZCONSTOL_ID);
2036	>	if (globals->haveZconsTol()){
2037	>	zconsTol->setData(globals->getZconsTol());
2038	>	}
2039	>	else{
2040	>	double defaultZConsTol = 0.01;
2041	>	sprintf(painCave.errMsg,
2042	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2043	>	"\tOOPSE will use a default value of %f.\n"
2044	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2045	>	defaultZConsTol);
2046	>	painCave.isFatal = 0;
2047	>	simError();
2048	>
2049	>	zconsTol->setData(defaultZConsTol);
2050	>	}
2051	>	theInfo.addProperty(zconsTol);
2052	>
2053	>	//set Force Subtraction Policy
2054	>	StringData* zconsForcePolicy = new StringData();
2055	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2056	>
2057	>	if (globals->haveZconsForcePolicy()){
2058	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2059	>	}
2060	>	else{
2061	>	sprintf(painCave.errMsg,
2062	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2063	>	"\tOOPSE will use PolicyByMass.\n"
2064	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2065	>	painCave.isFatal = 0;
2066	>	simError();
2067	>	zconsForcePolicy->setData("BYMASS");
2068	>	}
2069	>
2070	>	theInfo.addProperty(zconsForcePolicy);
2071	>
2072	>	//set zcons gap
2073	>	DoubleData* zconsGap = new DoubleData();
2074	>	zconsGap->setID(ZCONSGAP_ID);
2075	>
2076	>	if (globals->haveZConsGap()){
2077	>	zconsGap->setData(globals->getZconsGap());
2078	>	theInfo.addProperty(zconsGap);
2079	>	}
2080	>
2081	>	//set zcons fixtime
2082	>	DoubleData* zconsFixtime = new DoubleData();
2083	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
2084	>
2085	>	if (globals->haveZConsFixTime()){
2086	>	zconsFixtime->setData(globals->getZconsFixtime());
2087	>	theInfo.addProperty(zconsFixtime);
2088	>	}
2089	>
2090	>	//set zconsUsingSMD
2091	>	IntData* zconsUsingSMD = new IntData();
2092	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2093	>
2094	>	if (globals->haveZConsUsingSMD()){
2095	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2096	>	theInfo.addProperty(zconsUsingSMD);
2097	>	}
2098	>
2099	>	//Determine the name of ouput file and add it into SimInfo's property list
2100	>	//Be careful, do not use inFileName, since it is a pointer which
2101	>	//point to a string at master node, and slave nodes do not contain that string
2102	>
2103	>	string zconsOutput(theInfo.finalName);
2104	>
2105	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2106	>
2107	>	StringData* zconsFilename = new StringData();
2108	>	zconsFilename->setID(ZCONSFILENAME_ID);
2109	>	zconsFilename->setData(zconsOutput);
2110	>
2111	>	theInfo.addProperty(zconsFilename);
2112	>
2113	>	//setup index, pos and other parameters of z-constraint molecules
2114	>	nZConstraints = globals->getNzConstraints();
2115	>	theInfo.nZconstraints = nZConstraints;
2116	>
2117	>	zconStamp = globals->getZconStamp();
2118	>	ZConsParaItem tempParaItem;
2119	>
2120	>	ZConsParaData* zconsParaData = new ZConsParaData();
2121	>	zconsParaData->setID(ZCONSPARADATA_ID);
2122	>
2123	>	for (int i = 0; i < nZConstraints; i++){
2124	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2125	>	tempParaItem.zPos = zconStamp[i]->getZpos();
2126	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2127	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
2128	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2129	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2130	>	zconsParaData->addItem(tempParaItem);
2131	>	}
2132	>
2133	>	//check the uniqueness of index
2134	>	if(!zconsParaData->isIndexUnique()){
2135	>	sprintf(painCave.errMsg,
2136	>	"ZConstraint Error: molIndex is not unique!\n");
2137	>	painCave.isFatal = 1;
2138	>	simError();
2139	>	}
2140	>
2141	>	//sort the parameters by index of molecules
2142	>	zconsParaData->sortByIndex();
2143	>
2144	>	//push data into siminfo, therefore, we can retrieve later
2145	>	theInfo.addProperty(zconsParaData);
2146	>	}
2147	>
2148	>	void SimSetup::makeMinimizer(){
2149	>
2150	>	OOPSEMinimizer* myOOPSEMinimizer;
2151	>	MinimizerParameterSet* param;
2152	>	char minimizerName[100];
2153	>
2154	>	for (int i = 0; i < nInfo; i++){
2155	>
2156	>	//prepare parameter set for minimizer
2157	>	param = new MinimizerParameterSet();
2158	>	param->setDefaultParameter();
2159	>
2160	>	if (globals->haveMinimizer()){
2161	>	param->setFTol(globals->getMinFTol());
2162	>	}
2163	>
2164	>	if (globals->haveMinGTol()){
2165	>	param->setGTol(globals->getMinGTol());
2166	>	}
2167	>
2168	>	if (globals->haveMinMaxIter()){
2169	>	param->setMaxIteration(globals->getMinMaxIter());
2170	>	}
2171	>
2172	>	if (globals->haveMinWriteFrq()){
2173	>	param->setMaxIteration(globals->getMinMaxIter());
2174	>	}
2175	>
2176	>	if (globals->haveMinWriteFrq()){
2177	>	param->setWriteFrq(globals->getMinWriteFrq());
2178	>	}
2179	>
2180	>	if (globals->haveMinStepSize()){
2181	>	param->setStepSize(globals->getMinStepSize());
2182	>	}
2183	>
2184	>	if (globals->haveMinLSMaxIter()){
2185	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2186	>	}
2187	>
2188	>	if (globals->haveMinLSTol()){
2189	>	param->setLineSearchTol(globals->getMinLSTol());
2190	>	}
2191	>
2192	>	strcpy(minimizerName, globals->getMinimizer());
2193	>
2194	>	if (!strcasecmp(minimizerName, "CG")){
2195	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2196	>	}
2197	>	else if (!strcasecmp(minimizerName, "SD")){
2198	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2199	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2200	>	}
2201	>	else{
2202	>	sprintf(painCave.errMsg,
2203	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2204	>	painCave.isFatal = 0;
2205	>	simError();
2206	>
2207	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2208	>	}
2209	>	info[i].the_integrator = myOOPSEMinimizer;
2210	>
2211	>	//store the minimizer into simInfo
2212	>	info[i].the_minimizer = myOOPSEMinimizer;
2213	>	info[i].has_minimizer = true;
2214	>	}
2215	>
2216		}

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